andi1

Usage

Overview

andi estimates the evolutionary distance between closely related genomes. For this andi reads the input sequences from FASTA files and computes the pairwise anchor distance. The idea behind this is explained in a paper by Haubold et al. (2015).

Output

The output is a symmetrical distance matrix in PHYLIP format, with each entry representing divergence with a positive real number. A distance of zero means that two sequences are identical, whereas other values are estimates for the nucleotide substitution rate (Jukes-Cantor corrected). For technical reasons the comparison might fail and no estimate can be computed. In such cases nan is printed. This either means that the input sequences were too short (<200bp) or too diverse (K>0.5) for our method to work properly.

Options

-b INT, --bootstrap=INT

Compute multiple distance matrices, with n-1 bootstrapped from the first. See the paper Klötzl & Haubold (2016) for a detailed explanation.

--file-of-filenames=FILE

Usually, andi is called with the filenames as commandline arguments. With this option the filenames may also be read from a file itself, with one name per line. Use a single dash ('-') to read from stdin.

-j, --join

Use this mode if each of your FASTA files represents one assembly with numerous contigs. andi will then treat all of the contained sequences per file as a single genome. In this mode at least one filename must be provided via command line arguments. For the output the filename is used to identify each sequence.

-l, --low-memory

In multithreaded mode, andi requires memory linear to the amount of threads. The low memory mode changes this to a constant demand independent from the used number of threads. Unfortunately, this comes at a significant runtime cost.

-m MODEL, --model=MODEL

Set the nucleotide evolution model to one of 'Raw', 'JC', 'Kimura', or 'LogDet'. By default the Jukes-Cantor correction is used.

-p FLOAT

Significance of an anchor; default: 0.025.

--progress[=WHEN]

Print a progress bar. WHEN can be 'auto' (default if omitted), 'always', or 'never'.

-t INT, --threads=INT

The number of threads to be used; by default, all available processors are used.
Multithreading is only available if andi was compiled with OpenMP support.

--truncate-names

By default andi outputs the full names of sequences, optionally padded with spaces, if they are shorter than ten characters. Names longer than ten characters may lead to problems with downstream tools. With this switch names will be truncated.

-v, --verbose

Prints additional information, including the amount of found homology. Apply multiple times for extra verboseness.

-h, --help

Prints the synopsis and an explanation of available options.

--version

Outputs version information and acknowledgments.

Acknowledgments

1) andi: Haubold, B. Klötzl, F. and Pfaffelhuber, P. (2015). andi: Fast and accurate estimation of evolutionary distances between closely related genomes, Bioinformatics 31.8.
2) Algorithms: Ohlebusch, E. (2013). Bioinformatics Algorithms. Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. pp 118f.
3) SA construction: Mori, Y. (2005). libdivsufsort, unpublished.
4) Bootstrapping: Klötzl, F. and Haubold, B. (2016). Support Values for Genome Phylogenies, Life 6.1.